Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate WP_018123537.1 B149_RS0102265 carbamoyl-phosphate synthase large subunit
Query= SwissProt::Q42601
(1187 letters)
>NCBI__GCF_000375485.1:WP_018123537.1
Length = 1077
Score = 1239 bits (3207), Expect = 0.0
Identities = 635/1092 (58%), Positives = 814/1092 (74%), Gaps = 26/1092 (2%)
Query: 94 KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
KR+DLKKIM++G+GPIVIGQACEFDYSGTQA KAL+EEGYEV+L+NSNPA+IMTDPE A+
Sbjct: 3 KRSDLKKIMLIGSGPIVIGQACEFDYSGTQALKALKEEGYEVVLVNSNPASIMTDPELAD 62
Query: 154 RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
RTYI P+ PE V ++IEKERPDALLPT+GGQT LN A+A+AE G L+K+GVELIGA L A
Sbjct: 63 RTYIEPIEPETVARIIEKERPDALLPTLGGQTGLNTALAVAEMGVLDKFGVELIGADLDA 122
Query: 214 IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
I+KAE RELF+ AM+NIGL P SGI D+ + EK+ FP+IIRPAFTLGGTGGG+
Sbjct: 123 IQKAESRELFRKAMENIGLTVPLSGIARNQDDIREWGEKLS-FPIIIRPAFTLGGTGGGV 181
Query: 274 AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
AYN EE I G+AAS S+V++E+S+LGWKEYELEVMRD DN VIICSIEN+DPMG
Sbjct: 182 AYNMEELIEIASKGIAASMQSEVMLEESILGWKEYELEVMRDSKDNCVIICSIENLDPMG 241
Query: 334 VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
VHTGDS+TVAPAQTLTD EYQ++RD S+AI+REIGVE GGSNVQFAVNP +G++++IEMN
Sbjct: 242 VHTGDSVTVAPAQTLTDDEYQKMRDASLAIMREIGVETGGSNVQFAVNPENGDLVVIEMN 301
Query: 394 PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
PRVSRSSALASKATGFPIAK+AAKL+VGYTLD+IPNDITR+T ASFEP+IDY V KIPRF
Sbjct: 302 PRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITRETMASFEPAIDYCVIKIPRF 361
Query: 454 AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
FEKFPG++ L+T MKSVGE+MA+GRTF+E+ QK LRSLE G G G + ++ + + D
Sbjct: 362 TFEKFPGAEDYLSTAMKSVGETMAIGRTFKEALQKGLRSLETGHVGLG-KRFEKCEIERD 420
Query: 514 QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
+L LR PN R+ A+ AM+ GM ++E+++ + +D WFL Q ++++D+E+ L+ +
Sbjct: 421 ELLQLLRKPNSQRLFALRNAMRCGMSLEEVHDATWIDPWFLGQFRDVLDMEERLIEFGIK 480
Query: 574 EITKED-------LYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAE 626
E +E L + K+ G+SD Q+A KT+E+ VR R+ LG+ P+Y VDTCAAE
Sbjct: 481 EGIEESTPELPAILRKAKEYGYSDAQLATMWKTSEDAVRNLRLKLGIRPTYYLVDTCAAE 540
Query: 627 FEAHTPYMYSSYDVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYET 686
FEA+TPY YS+Y+ E P +K++ILGGGPNRIGQGIEFDYCCCH+SF L++ G ++
Sbjct: 541 FEAYTPYYYSTYEGGDEIEPAEGRKIVILGGGPNRIGQGIEFDYCCCHSSFMLREMGIKS 600
Query: 687 IMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKH 746
IM+NSNPETVSTDYDTSDRLYFEPLT EDV+N+ID EKPDG++VQFGGQTPL LA+
Sbjct: 601 IMVNSNPETVSTDYDTSDRLYFEPLTFEDVMNIIDFEKPDGVVVQFGGQTPLNLAI---- 656
Query: 747 YLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALA 806
L AG V + GTSPD+ID AEDRERF +L++L ++QP G A S +A
Sbjct: 657 --------RLMNAG-VPLIGTSPDAIDRAEDRERFKQLLNKLHLKQPPNGTAMSMVEARE 707
Query: 807 IAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEID 866
IA+++G+P+V+RPSYVLGGR M+IVY Y + V PE P L+DK+L A+E+D
Sbjct: 708 IAEKLGFPLVLRPSYVLGGRGMDIVYSMEDFERYFRESALVSPEHPTLIDKFLEYAVEVD 767
Query: 867 VDTLTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNV 926
VD L D V IGG+MEHIE+AG+HSGDSA +LP ++ ++ I TT +A +L V
Sbjct: 768 VDALCDG-EQVYIGGVMEHIEEAGIHSGDSASVLPPYSLSPEMVREIERQTTAMAIELGV 826
Query: 927 CGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFEK 986
GLMN QYAI +V+++E NPRASRTVPFVSKA P+AK A VM G+ +KDL
Sbjct: 827 VGLMNVQYAI-KDDEVYVIEVNPRASRTVPFVSKATAVPMAKLATRVMMGEKIKDLKPWS 885
Query: 987 EVIPKHVSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPL 1046
H+S+KE+VFPF +F DV+LGPEMRSTGEVM I F A+ +Q+AAGQKLP
Sbjct: 886 MRKKGHISIKESVFPFNRFPNVDVLLGPEMRSTGEVMGIDESFGLAYMKSQLAAGQKLPK 945
Query: 1047 SGTVFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEG-RPH 1105
G VF+S+ND K + F ++GF I+AT GTA +LE KG+ V+RV K+HEG RP+
Sbjct: 946 GGNVFVSVNDWDKNKVLLPVRDFQDMGFSILATGGTADYLEEKGVKVQRVYKVHEGQRPN 1005
Query: 1106 AADMVANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKS 1165
D++ NG I L+L T SG D + +RQ L Y +P TT++GA A A+ I L+
Sbjct: 1006 VVDLIKNGDIDLVLNTPSGKK-TVGDSKMIRQATLLYNIPYTTTISGARAVAQAIYELRE 1064
Query: 1166 SAIKMTALQDFF 1177
+ + + ++Q+++
Sbjct: 1065 TGLVVKSIQEYY 1076
Lambda K H
0.317 0.133 0.383
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3124
Number of extensions: 130
Number of successful extensions: 20
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1187
Length of database: 1077
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1031
Effective search space: 1176371
Effective search space used: 1176371
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)
Align candidate WP_018123537.1 B149_RS0102265 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.aa/TIGR01369.hmm
# target sequence database: /tmp/gapView.3544.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01369 [M=1052]
Accession: TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1511.2 0.0 0 1511.0 0.0 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018123537.1 B149_RS0102265 carbamoyl-phospha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123537.1 B149_RS0102265 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1511.0 0.0 0 0 1 1052 [] 2 1059 .. 2 1059 .. 0.98
Alignments for each domain:
== domain 1 score: 1511.0 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+d+kk+++iGsGpivigqA+EFDYsG+qalkalkeeg+evvLvnsn+A +mtd+elad++YieP
lcl|NCBI__GCF_000375485.1:WP_018123537.1 2 PKRSDLKKIMLIGSGPIVIGQACEFDYSGTQALKALKEEGYEVVLVNSNPASIMTDPELADRTYIEP 68
6899*************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+++e+v++iiekErpDa+l+tlGGqt+Ln a+ + e+GvL+k+gv+l+G++++ai+kae+Re+F++a
lcl|NCBI__GCF_000375485.1:WP_018123537.1 69 IEPETVARIIEKERPDALLPTLGGQTGLNTALAVAEMGVLDKFGVELIGADLDAIQKAESRELFRKA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
+++i++ v+ s i++++++ e e++ +P+i+R+aftlgGtG+g+a+n+eel e+++k+++as+ +
lcl|NCBI__GCF_000375485.1:WP_018123537.1 136 MENIGLTVPLSGIARNQDDIREWGEKLSFPIIIRPAFTLGGTGGGVAYNMEELIEIASKGIAASMQS 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
+v++e+s+ gwkE+E+Ev+RDskdnc+i+c+iEnlDp+GvHtGds++vaP+qtLtd+eyq++Rdasl
lcl|NCBI__GCF_000375485.1:WP_018123537.1 203 EVMLEESILGWKEYELEVMRDSKDNCVIICSIENLDPMGVHTGDSVTVAPAQTLTDDEYQKMRDASL 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+i+re+gve++ +nvqfa++Pe+ ++vviE+npRvsRssALAskAtG+PiAk+aaklavGy+Lde++
lcl|NCBI__GCF_000375485.1:WP_018123537.1 270 AIMREIGVETGgSNVQFAVNPENGDLVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIP 336
*********988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t+et+AsfEP++DY+v+kiPr+ ++kf ++++ l+t mksvGE maigrtf+ealqk+lrsle+
lcl|NCBI__GCF_000375485.1:WP_018123537.1 337 NDITRETMASFEPAIDYCVIKIPRFTFEKFPGAEDYLSTAMKSVGETMAIGRTFKEALQKGLRSLET 403
******************************************************************* PP
TIGR01369 402 kllglklk.ekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvel 467
+ +gl ++ ek +++++el + l+kpn +Rlfa+ +a+r g+s+eev+++t id +fl ++++++++
lcl|NCBI__GCF_000375485.1:WP_018123537.1 404 GHVGLGKRfEKCEIERDELLQLLRKPNSQRLFALRNAMRCGMSLEEVHDATWIDPWFLGQFRDVLDM 470
****655425677888999************************************************ PP
TIGR01369 468 ekeleeeklk....elkke...llkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtv 527
e++l e +k e + e l+kak++G+sd+q+a+++k+se++vr+lr +lgi p++ vDt+
lcl|NCBI__GCF_000375485.1:WP_018123537.1 471 EERLIEFGIKegieESTPElpaILRKAKEYGYSDAQLATMWKTSEDAVRNLRLKLGIRPTYYLVDTC 537
***998855522223333322279******************************************* PP
TIGR01369 528 aaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktili 594
aaEfea tpY+Ystye+ d++e e +k+++lG+Gp+Rigqg+EFDyc+ h++ lre+g+k+i++
lcl|NCBI__GCF_000375485.1:WP_018123537.1 538 AAEFEAYTPYYYSTYEGG-DEIEPAEGRKIVILGGGPNRIGQGIEFDYCCCHSSFMLREMGIKSIMV 603
******************.************************************************ PP
TIGR01369 595 nynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsa 661
n+nPEtvstDyd++drLyFe+lt+edv++ii+ ek++gv+vq+gGqt+lnla +l +agv+++Gts+
lcl|NCBI__GCF_000375485.1:WP_018123537.1 604 NSNPETVSTDYDTSDRLYFEPLTFEDVMNIIDFEKPDGVVVQFGGQTPLNLAIRLMNAGVPLIGTSP 670
******************************************************************* PP
TIGR01369 662 esidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneee 728
++idraEdRe+F++ll++l++kqp + +a s+ ea+eia+++g+P+++RpsyvlgGr+m+iv+++e+
lcl|NCBI__GCF_000375485.1:WP_018123537.1 671 DAIDRAEDRERFKQLLNKLHLKQPPNGTAMSMVEAREIAEKLGFPLVLRPSYVLGGRGMDIVYSMED 737
******************************************************************* PP
TIGR01369 729 leryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqk 795
+ery++e + vs+e+P lidk+le avEvdvDa++dge+v+i g++eHiEeaG+HsGDs+ vlpp +
lcl|NCBI__GCF_000375485.1:WP_018123537.1 738 FERYFRESALVSPEHPTLIDKFLEYAVEVDVDALCDGEQVYIGGVMEHIEEAGIHSGDSASVLPPYS 804
******************************************************************* PP
TIGR01369 796 lseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavk 862
ls e++++i+++++++a el v+Gl+n+q+++kd+evyviEvn+RasRtvPfvska+ vp++kla++
lcl|NCBI__GCF_000375485.1:WP_018123537.1 805 LSPEMVREIERQTTAMAIELGVVGLMNVQYAIKDDEVYVIEVNPRASRTVPFVSKATAVPMAKLATR 871
******************************************************************* PP
TIGR01369 863 vllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkal 929
v++g+k+++l+ ++ k+ ++++k++vf+f+++ +vdv+lgpem+stGEvmgi++++ a++k++
lcl|NCBI__GCF_000375485.1:WP_018123537.1 872 VMMGEKIKDLKP--WSMRKKGHISIKESVFPFNRFPNVDVLLGPEMRSTGEVMGIDESFGLAYMKSQ 936
*********987..66777789********************************************* PP
TIGR01369 930 laskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseea. 995
la+++k++k g+v++sv+d dk+++l ++ ++++g++++at gta++lee+g+k++ v+kv+e +
lcl|NCBI__GCF_000375485.1:WP_018123537.1 937 LAAGQKLPKGGNVFVSVNDWDKNKVLLPVRDFQDMGFSILATGGTADYLEEKGVKVQRVYKVHEGQr 1003
*************************************************************999765 PP
TIGR01369 996 ekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealleal 1052
+++++l+k+++i+lv+n++s +kk++ ++++ir++++ y++p+ t++++a+a+++a+
lcl|NCBI__GCF_000375485.1:WP_018123537.1 1004 PNVVDLIKNGDIDLVLNTPS-GKKTVGDSKMIRQATLLYNIPYTTTISGARAVAQAI 1059
99***************998.77788999***********************99985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1077 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 12.13
//
[ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory